Pittsburgh Post-Gazette Article (Dec. 9, 2005)
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Publications
This is a list of publications originating from our group.
- Robinson CM, O’Dee D, Hamilton T, Nau GJ. " IL-27 Antagonizes IL-18-mediated IFN-γ Production by Mycobacterium tuberculosis-infected Human Macrophages" . J Innate Immunity 2009. In press.
- FR Toapanta and TM Ross. "Impaired Immune Responses in the Lungs of Aged Mice Following Influenza Infection" . In Press, 2009
- Carlson PE Jr, Horzempa J, O’Dee D, Robinson CM, Neophytou P, Labrinidis A, Nau GJ. "Global transcriptional response to spermine, a component of the intra-macrophage environment, reveals regulation of Francisella gene expression through insertion sequence elements' . J Bacteriology 2009 191:6855-6894
- Denise E. Kirschner and Jennifer J. Linderman "Mathematical and computational approaches can complement experimental studies of host pathogen interactions" . Cellular Microbiology (2009) 11:531-539
- Tchagang, A.B., Bui, K.V., McGinnis, T. and Benos, P.V. "Extracting biologically significant patterns from short time series gene expression data" . BMC Bioinformatics (2009), 10:255
- Y. Lu, R. Rosenfeld, G.J. Nau, and Z. Bar-Joseph. "Cross species expression analysis of innate immune response." Proceedings of The 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), in press, 2009
- Ray, JCJ, JL Flynn, DE Kirschner "Synergy between individual tumor necrosis factor-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection" J. Immunol, 182:3706-3717, 2009
- Y. Lu, P. Huggins, and Z. Bar-Joseph. "Cross species analysis of microarray expression data". Bioinformatics (in press) 2009; published online
- Y. Lu, R. Rosenfeld, G.J. Nau, and Z. Bar-Joseph. "Cross species expression analysis of innate immune response. " Proceedings of The 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), in press, 2009.
- Brower-Sinning R, Carter DM, Crevar CJ, Ghedin E, Ross TM, Benos PV. "The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus." Genome Biol. 2009 10
- Robinson CM, Nau GJ. "Interleukin-12 and Interleukin-27 Regulate Macrophage Control of Mycobacterium tuberculosis" . J Infect Dis. 2008 198:359-66. PMC2761687
- Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z. "A probabilistic generative model for GO enrichment analysis Nucleic Acids" Res. 2008
- Ray, J. C., J. Wang, J. Chan, and D. E. Kirschner. "The timing of TNF and IFN-gamma signaling affects macrophage activation strategies during Mycobacterium tuberculosis infection." J Theor Biol 252:24-38, 2008
- Horzempa J, Carlson PE Jr, O'Dee DM, Shanks RM, Nau GJ.: "Global transcriptional response to mammalian temperature provides new insight into Francisella tularensis pathogenesis" BMC Microbiol. 2008
- Lin TH, Kaminski N, Bar-Joseph Z." Alignment and classification of time series gene expression in clinical studies" Bioinformatics. 2008
Qinglan Li, Alexandros Labrinidis, and Panos K. Chrysanthis. "ViP: a User-centric View-based Annotation Framework for Scientific Data", Proc. of the 20th International Conference on Scientific and Statistical Database Management (SSDBM'08), 295-312, Hong Kong, China, July 2008
- S. Ta'asan and R. Gandlin, BioLogic: "A Mathematical Modeling Framework for immunologists". A chapter book in Systems Biology, Editor Ivan Maly, Humana Press, Methods in Molecular Biology series, (in press)
- Bauer, A, Marino, S, Hogue, I and Kirschner, D. "The effects of HIV-1 on latent TB infection." (in press) Mathematical Modelling of Natural Phenomena 2008.
- Hogue, I, Bajaria, S, Qin, S, Fallert, B, Reinhart, T and Kirschner, D. "The Dual Role of Dendritic cells in the Immune Response to HIV-1 Infection." Journal of General Virology, 89(Pt 9):2228-39, 2008.
- Chang, S, Linderman, JL and Kirschner, D. "The effect of multiple polymorphisms on antigen presentation and susceptibility to M. tuberculosis infection" , Infection and Immunity, pp 3221–3232, 2008.
- Soumya, D. Chakravarty, SD, Zhu, G, Tsai, MC, Mohan, VP, Marino, S, Kirschner, DE, Huang, B, Flynn, J and John Chan. "Tumor Necrosis Factor Blockade in Chronic Murine Tuberculosis Leads to Granuloma Disorganization and Enhanced Pulmonary Inflammation Infection and Immunity" , 76(3): 916–926, 2008.
- Marino; S, Hogue; IB, Ray; CJ, Denise Kirschner. "A Methodology For Performing Global Uncertainty And Sensitivity Analysis In Systems Biology", Journal of Theoretical Biology, 254(1), 2008
- Ray, JCJ, Chan, J and Kirschner, D. "Competing requirements for macrophage function contribute to intracellular survival of Mycobacterium tuberculosis", (in press) The Journal of Theoretical Biology, 2008
- T. H. Lin, N. Kaminski and Z. Bar-Joseph. "Alignment and Classification of Time Series Gene Expression in Clinical Studies" . Bioinformatics (ISMB), 24(13):i147-i155, 2008.
- Ernst, Q.K. Beg, K. Kay, G. Balazsi, Z. Oltvai and Z. Bar-Joseph. "A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli" . PLoS Computational Biology, 4(3): e1000044, 2008 3
- Marino, S, Sud, D, Flynn,J Kirschner, D. "Differences in reactivation of tuberculosis induced from anti-TNF treatments are based on bioavailability in granulomatous tissue" . PLOS Computational Biology, 3(10): e194, 2007.
- Marino, S, Baretta, E and Kirschner, D. "The role of delays in innate and adaptive immunity to intracellular bacteria infections" Mathematical Biosciences and Engineering, 261-286, Volume 4,2007.
- HL Plessner, PL Lin, T Khono, J Louie, D Kirschner, J Chan and JL Flynn. "Neutralization of TNF by antibody but not by TNF receptor fusion molecule exacerbates chronic murine tuberculosis" Journal of Infectious Diseases, 195(11):1643-50, 2007
- Morel PA, S Ta'asan, BF Morel, DE Kirschner and JL Flynn. "New insights into mathematical modeling of the immune system". 2006. Immunol. Res. 36:157-166
- Mahony S, Auron PE, Benos PV: "DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies" . PLoS Comput Biol 2007, 3(3):e61;
- J. Ernst, O. Vainas, C.T. Harbison, I. Simon and Z. Bar-Joseph. "Reconstructing dynamic regulatory maps Molecular Systems Biology " , 3:74, 2007
- Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z: "Combined analysis reveals a core set of cycling genes" . Genome Biol 2007, 8(7):R146.
- Mahony S, Benos PV: "STAMP: a web tool for exploring DNA-binding motif similarities" . Nucleic Acids Res 2007, 35(Web Server issue):W253-258
- Mahony S, Auron PE, Benos PV: " Inferring protein-DNA dependencies using motif alignments and mutual information" . Bioinformatics 2007, 23(13):i297-304
- Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, et al: "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences" . Nature 2007, 447(7141):167-177
- Mahony S, Corcoran DL, Feingold E, Benos PV: "Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome" . Genome Biol 2007, 8(5):R84.
- N. Kaminski and Z. Bar-Joseph. "A patient-gene model for temporal expression profiles in clinical studies" . Journal of Computational Biology, 14(3), pp 324-338, 2007.
- J. Ernst and Z. Bar-Joseph. "STEM: a tool for the analysis of short time series gene expression data" . BMC Bioinformatics, 7:19, 2006.
- Y. Shi, M. Klustein, I. Simon, T. Mitchell, Z. Bar-Joseph. "Continuous hidden process model for time series expression experiments" . Bioinformatics (Proceedings of ISMB 2007), 23(13), pp i459-i467, 2007
- Martinez, H.M. "Detecting pseudoknots and other local base-pairing structures in RNA sequences" . Methods in enzymology, 183, 306-317, 1990
- Y. Lu, R. Rosenfeld, and Z. Bar-Joseph. "Identifying cycling genes by combining sequence homology and expression data" . Bioinformatics (Proceedings of ISMB), 22(14):e314-22 2006